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Odo, Kira Nerys, and Jadzia Dax sit having breakfast in the mess hall of the USS Defiant. Lieutenant Commander Dax states that she can't wait to sleep in her own bed, remarking on the uncomfortable bunks on the Defiant. Major Kira says that she could use a visit to the Golian Spa. Dax comments that Kira and Shakaar should both go, to which Kira says that she and Shakaar aren't seeing each other anymore. Odo, who has had feelings for Kira for a long time, asks about the breakup. Kira says that she and Shakaar went to the Kenda Shrine on Bajor to ask the Prophets if they were meant to walk the same path. Upon hearing that the Prophets said no, Dax remarks that Kira makes it sound final. Kira responds that people are either meant to be together or not. Dax states that any relationship can work if the partners really work at it. Odo, still contemplating the ramifications of the conversation, says that he has no opinion on the subject and hastily leaves. Kira wonders if he is all right and Dax reminds her that the subject of relationships has always made Odo uncomfortable.

Later, on the bridge of the Defiant, mugs of raktajino are being passed around to everyone. CaptainBenjamin Sisko declines, saying that he is trying to cut down. ChiefMiles O'Brien then begins talking about a doll house he is making for Molly's birthday, lamenting the fact that even with a micro-lathe he might not get it done in time. Commander Dax then begins to get some readings on her console. An energy barrier of some kind is encasing the fourth planet of a nearby star system. Major Kira begins scanning and states that there could be lifeforms on the surface of the planet, but the interference from the energy barrier is making it difficult to be certain. Dax seems more interested, wanting to know how the lifeforms adapted to the quantum fluctuations in the barrier. While it is an intriguing scientific possibility, O'Brien wants to push off an investigation until the next time they go by this planet. Dax says that the interference is intensifying so that in a few weeks, a probe would not make it through the barrier. Dax knows that everyone wants to go home, but this is the only chance. After ordering modifications to the shields, Sisko gives the go ahead.

As the Defiant enters the barrier, the ship starts to shake. Dax tries to adjust the shields, but the shaking gets more violent. Energy begins to arc across the bridge consoles and Major Kira is struck by a discharge. While caught in the energy, it appears as if there were two Kiras, slightly out of phase with each other. After a moment, the energy dissipates and the ship is through the barrier. Sisko calls Dr.Julian Bashir to the bridge to check on Kira. O'Brien then tells the captain that the inertial dampers are off-line and the gyromagnetic stabilizers have depolarized, stranding the Defiant in orbit for a few days. Suddenly, Lieutenant Commander Worf says that they are being hailed from the surface. Upon scanning the surface he also reports that there are several settlements on the planet, with approximately eight thousand inhabitants – Human inhabitants. Stunned, Sisko answers the hail. A Human woman and a Trill man welcome them to Gaia, calling Captain Sisko by name. The woman says that they have been expecting them. The man speaks up, saying it is a long story. He invites them to beam down and talk about it over some raktajino, and then catches himself. "I forgot. You're trying to cut down."

Yedrin Dax

Miranda O'Brien

Sisko, Dax, Worf, and O'Brien beam down into a cluster of adobe-like buildings, surrounded by farmland. Children who were playing a game with a ball stop and stare at the newcomers. The two people who made the hail introduce themselves as Miranda O'Brien and Yedrin Dax. Sisko asks for an explanation. Miranda tells them that the settlement was founded by the crew of a Starfleet vessel that crashed on the planet two centuries prior. She reveals that the ship that crashed was the USS Defiant. In two days, when Captain Sisko tries to leave orbit, Miranda says that they will be thrown back two hundred years into the past. The people they see now are the crew's descendants.

Yedrin sees that the Starfleet officers are skeptical and tells Jadzia to scan him. With her tricorder, she finds the Daxsymbiont in Yedrin. It was passed down to Jadzia's descendants for three generations. He also tells her to scan Miranda. Jadzia finds that Miranda's DNA is similar to Miles', making her an O'Brien. Miranda also states that she is also a Tannenbaum, a descendant of Rita Tannenbaum, an ensign on the Defiant's engineering crew. Miranda then relates to Miles that they were trapped two hundred years in the past without any chance of seeing their families or friends. Yedrin says that Miles was the last to give up hope, but he eventually married Rita ten years after the Defiant crashed. Yedrin still sees doubt on Sisko's face and offers to tell him something that only Curzon would know. He begins a story about a dancer on Pelios Station, but Sisko cuts him off as both Yedrin and Jadzia smile knowingly. A young boy named Gabriel asks Worf if he is the son of Mogh and if he can kill someone just by looking at them. Worf responds "Only when I am angry." The boy's eyes get wide and he runs off.

Miranda then directs them into a nearby structure. As they enter, two girls are sitting at a table near a viewscreen, salvaged from the bridge of the Defiant. The girls are doing schoolwork with the help of the image of Quark. Yedrin says that Jadzia designed the educational program, saying she thought Quark would make a great math teacher. Jadzia comments on one of the girl's spots. Lisa says that most people don't have them as most of their ancestors were Human. She says that they make her special. The other girl, Molly, says it is just genetics, like Torvin's cranial ridges. Miles is taken aback at the name of the girl and Yedrin says that the name was passed down through the O'Brien line. Worf asks if they ever tried to send out a distress call. However, being two hundred years in the past and in the Gamma Quadrant, it was never done. Lisa then says that their ancestors decided to make the planet their new home, naming it Gaia. Molly gets in on the story saying that their ancestors needed to build a shelter quickly before winter came. The structure they are in was built and all forty-eight crewmen had to sleep in it.

Sisko seizes on the number and confronts Yedrin. Yedrin explains that the energy discharge that struck Kira damaged her neural pathways. The Defiant doesn't have advanced enough medical equipment that Bashir needs to repair the damage, and therefore Kira died a few weeks after the crash. Miranda tells the girls to leave, to spare them from an adult conversation, and sends them to their parents to help with the planting. Sisko states that they need to get Kira back to the station as soon as the Defiant is repaired. Yedrin agrees. Worf says that if they escape from the planet, the inhabitants' timeline will collapse and everything will cease to exist. Yedrin, however, says that he has a plan. The key was Kira. The energy discharge caused a subspace doubling effect. He says that for an instant, every molecule in Kira's body had a corresponding quantum duplicate. If certain modifications to the Defiant's systems were made, they could amplify the doubling effect and duplicate the entire ship. One ship would be sent back in time and one would pass through the barrier unaffected. From the logs he retrieved, Yedrin says that the Defiant encountered a temporal anomaly thirty-nine hours after arriving in orbit. Yedrin says that there are eight thousand people on the planet and this plan is their only choice. Sisko orders Jadzia to evaluate the plan and, if it is sound, begin the modifications. Yedrin thanks Sisko, to which Sisko says "Anything for you… Old man."

Back aboard the Defiant, Kira is resting on a bio-bed while Bashir is scanning a vat containing Odo. He puts Odo into a stasis device, telling Kira that because of the quantum fluctuations in the barrier, Odo can't hold his shape. Bashir says that Odo will be fine, but Kira needs to undergo a complete neural pathway induction when they get back to the station. Kira says that she feels fine. As he turns to leave, Kira asks where he is going. Bashir states that he wants to go down to the planet and meet his descendants. Kira looks at the stasis device, and turns when the doors open to admit a person who looks like Odo. He is dressed like the colonists and his facial features are more defined, but it is Odo, two hundred years older than the one sitting in the device. Odo explains that he learned to counter the barrier's effects and that he has gotten better at shape-shifting over the years. Odo then says that she is as beautiful as he remembered. Kira is somewhat shocked by this, and is even more shocked when Odo says that he loves her and has always loved her.

Kira begins questioning Odo about this revelation, saying that she never knew. Odo did everything he could to make sure she didn't find out. Kira begins saying how hard it must have been for him every time she came to him for advice about Bareil and Shakaar. Odo says that he wanted to be a good friend. He has been waiting two hundred years to say this, and all he wants is for Kira to spend some time with him on Gaia.

Back on the planet, Sisko is meeting some of his descendants, holding a baby. Miranda says that the child has Sisko's eyes. Jadzia then calls Sisko with good news: she has gone over the sensor logs and Yedrin's plan will work. Sisko then holds the baby over his head and talks to her "Everything's going to be all right."

Brota, descendant of Worf

Nearby, Worf is inspecting the town well as Bashir walks up to him. Worf is making a survey of the settlement's infrastructure at the captain's request so that they can leave behind supplies. Bashir says that he was doing the same at the clinic. Bashir appears overly pleased with himself. He has met one of his descendants, his great-great-great-great-granddaughter – the doctor of the settlement. Suddenly, Gabriel comes running up to them shouting that "They're here!" The Klingons have arrived.

Three people are standing in the street, holding spears and wearing knives. Two of the Klingons appear Human, while the other only has faint forehead ridges. Brota greets Worf and states that they are the Sons of Mogh. They are Worf's descendants, some by blood and some by choice. They live as warriors. Gabriel then says that he wants to become a Son of Mogh, to which Parell says that when he is older, he can prove himself and take a Klingon name. Brota says that the Sons of Mogh are gathering to celebrate Worf's return. Worf honors them by saying he will feast with them.

In engineering, Jadzia and Yedrin are working on modifying the Defiant's systems. Yedrin smiles as Jadzia adjusts her hair, remembering that the summer after the crash, Jadzia cut it short and that Worf hated it. Yedrin then remembers promising to grow it back for the wedding, which Sisko performed. As they talk about the wedding, Jadzia asks if they were happy. Yedrin says that Worf is a good man, and that she will learn to handle him.

Back on Gaia, Miles is installing a new pump for the town well as Bashir stands talking with him. People from the Defiant are talking with their descendants, which disturbs him. Bashir is going on about his descendants and says that he ends up with Ensign Angie Kirby, a new crewman who just transferred aboard. Bashir then begins to talk about Miles and Rita Tannenbaum. Miles rounds on Bashir and states he doesn't want to talk about it. "I have a wife and kids back home." Seeing that he has touched on a sensitive subject, Bashir leaves Miles to his work, while Lisa and Molly look and laugh at him nearby.

Elsewhere on Gaia, Kira is praying over her own grave while Odo looks on. As Kira finishes, she comments "Praying over your own grave… that's got to be a new one." Odo says that if the Prophets were listening, they might be confused. Kira then talks about Yedrin's plan, saying that it is a little strange. She has always believed that people have one path and now, they are using technology to circumvent that. Odo says that he is in favor of the plan, Kira would get her treatment and the Gaia's timeline would get preserved. He then goes on to say that even though the plan won't change anything for him, the Odo on the Defiant won't have to lose her. Kira is touched by this.

Back at the settlement, Sisko and some children are tossing a baseball around. Jadzia walks up with a PADD and doesn't look happy. She presents evidence to Sisko that Yedrin faked the logs so that they would think that his plan would work. There was never going to be a duplicate Defiant, just one. If Jadzia hadn't figured it out, they would have been stranded and Kira would have died.

In the meeting hall, Sisko and Jadzia have confronted Yedrin. Jadzia accuses Yedrin of betraying them. Yedrin asks what they will do. When Sisko tells him, Yedrin pleads with him saying that if the Defiant doesn't go back in time, eight thousand people will cease to exist. Sisko explains that he can't deliberately maroon his crew. Yedrin tells Sisko to look around, see all of the things that his crew and their descendants will build. Jadzia asks about Kira, to which Yedrin asks if one life is too much to ask if it would mean saving eight thousand. Sisko explodes at Yedrin, demanding to know how he can make that decision. Yedrin replies saying that he is responsible, and looks to Jadzia. She was the one that insisted that the Defiant investigate the planet. She knew that she should have been more careful, but she wanted to make a huge discovery. And because of that, the Defiant was sent to the past, Kira died, and forty-eight people were stranded. Yedrin tells of guilt that has been passed down through Dax. He says that the community is his responsibility, and that for two centuries he has watched it grow. Sisko is moved by Yedrin's plight, but says that his people have a right to go home to their families and no one has the right to ask anyone to die.

Later that night, Worf and Kira are sitting near a fire pit. They both do not like what is going to happen. Although the colonists are milling around, the mood is somber. Only the children seem unaffected. Kira comments that everyone is going to die because she has to get treated for something she can't even tell she has. Worf tells her not to blame herself. Kira moves off to return to the Defiant. Nearby, Miranda is tending some plantings and seedlings. Gabriel mentions that everyone is quiet and asks what is wrong. Miranda tells him it is nothing to worry about, not able to tell him the truth. As Gabriel leaves, the Klingons approach Worf and tell him that there will be no feast. Worf asks them to join him at the fire. He tells them of the honor to know that his legacy has thrived. Brota tells of a beast that he killed with Worf's own mek'leth. They then tell him that their ceasing to exist will not earn them a place in Sto-vo-kor. They all then unsheathe their daggers and ask Worf to kill them. Worf hesitates, but then tells them that he will do what they ask tomorrow.

Kira is back at her grave. Odo finds her and asks her why she came back. She wanted to be sure that this was where she belonged. As she looks at him, she says that the path the Prophets have laid out for her ends on Gaia. Odo protests, but Kira stops him. She can't let the captain go through with his plan if it means that eight thousand people will cease to exist, even if she has to.

Sisko, Jadzia, Worf, Bashir, and Miles are sitting in the Defiant's mess hall, hearing what Kira has said. Bashir reminds her that if she doesn't go back to the station, she will die. Kira says that she has accepted this and if they don't take the Defiant back in time, they would be cheating fate. Miles dismisses this, saying he has a wife and children back on the station who need him. Kira states that the Prophets will take care of them, but Miles responds that he doesn't believe in them. Worf then comments that their families will survive either way, but the colonists will not. He says that if Kira is willing to sacrifice her life, he would be willing to remain on Gaia. Miles still refuses to consider staying and tells Worf that it would be easy for him, he never sees his son. Worf bristles as he tells Miles that he is afraid to face his destiny. As Miles continues to get exasperated, he turns to Jadzia, Bashir, and Sisko. He tells them that no one has the right to tell him that he can't go home to his family. When Sisko says that he is hearing what everyone has to say, Miles asks if they are actually considering going back in time. Sisko seems unsettled by the arguments, but finally turns to Kira to say that they are not. Kira protests, but Sisko is adamant as he dismisses them.

As Jadzia and Worf are walking through the settlement on Gaia, they contemplate what they are going to do. They come upon Sisko who is getting one last look around. Suddenly Gabriel comes running around the corner, almost hitting Sisko. When asked where he is going, Gabriel tells them that he is going to the fields for the planting. As the three Starfleet officers round the next corner, they see several colonists getting ready to go to the fields. Yedrin sees them and says that planting day was always important.

Out in the fields, the colonists and most of the Defiant's crew are working at the various tasks of farming; plowing, fertilizing, planting and watering. Miles walks up, not doing any of the work, to give Sisko a status report. He says that the Defiant is ready to leave orbit. Molly, who is nearby, asks Miles if he is going to help. Miles says that he is busy, to which Molly says that he doesn't look busy. Sisko hands Miles a farming tool and tells him to get to work. People all around then notice that Worf is leading some of the Klingons towards them. Parell and Brota say that they do not see any enemy to fight, as Worf had told them. Worf says that they are trying to plant their fields before the sun sets and that time is their enemy. The Klingons exchange a look, and realize that Worf is offering them a challenge. The Klingons then join the colonists in their toil.

Molly

As Miles is working, he tells Molly that he has a little girl with the same name. When Molly asks if she can meet her, Miles looks sad knowing it can never happen. Moved by Molly, Miles goes to find Sisko and Kira. Miles tells them that they can't leave, they can't let all these people die. Sisko nods in agreement after a moment while Kira smiles sadly.

After their labors in the field, Sisko and Jadzia have told Yedrin and Miranda about their decision. Yedrin hands Jadzia a PADD which contains the navigational logs from the original crash. All Jadzia has to do is download them into the ship's auto-pilot and it should send the Defiant back to the right point in time.

On the Defiant, Odo is saying goodbye to Kira. Odo is trying to talk Kira out of her decision. She says that her decision isn't based on her, it is about all of the colonists and their descendants. Odo asks about the descendents that won't be born if the Defiant doesn't return to DS9 but seeing he can't change her mind, asks that if Kira knew about his feelings years ago would she do things differently. As Kira says that it maybe would have, she kisses him and turns to leave.

On the bridge, the crew is at their posts. Sisko asks if everyone has had a chance to record a message to their families. Everyone nods and Miles says that he has downloaded the recordings into a class 4 probe that will start transmitting a locating signal as soon as it clears the barrier. As the probe launches, Sisko orders helm control to be transferred to auto-pilot. The shields are raised as the Defiant breaks orbit. Scans show an unusual temporal signature, the anomaly that will take them back in time. The seconds count down as the Defiant heads towards impact when suddenly the ship veers away. The auto-pilot can't be overridden and the ship clears the barrier. Miles consults his console and reports that someone changed their flight plan, and that he didn't do it. Sisko orders a scan of the surface and Kira reports that there is no sign of the settlement or the inhabitants. Everything is gone.

Sisko and Jadzia are walking down a corridor as they discuss what happened. Whoever changed the flight plan knew their way around the Defiant's security systems. Jadzia says that it must have been one of the crew. Sisko then says that it could be someone who used to be part of the crew. This leads to them suspecting Yedrin, but Jadzia states that all he cared about was the settlement. Sisko supposes that he could have changed his mind. When Jadzia voices her lament that everyone they had met never existed, Sisko corrects her saying "They existed. And as long as we remember them, they always will."

An upset Kira is lying on her bed in her quarters when the door chimes. In walks Odo, who says that the other Odo came up to the ship and linked with him. Now he knows everything that the other Odo had told Kira. She remarks on his reactions from earlier when she talked of Shakaar. Odo had come to accept the fact that Kira was involved with someone else when suddenly all of that changed. Odo then tells her something else that the other Odo wanted her to know. He was responsible for changing the flight plan so that Kira didn't have to die. Kira is shocked by this and Odo says that the other Odo did it because he loved her. When she asks if that makes it right, he replies that he doesn't know but the other Odo thought so. Odo leaves her quarters as she considers everything that has happened.

"Are you the son of Mogh?"
"Yes, I am."
"Is it true you can kill someone just by looking at them?"
"Only when I am angry."

- Gabriel and Worf, at their first meeting

"They existed. As long as we remember them, they always will."

- Sisko, to Dax

"You said there was an enemy for us to fight."
"They are attempting to plant their fields before the sun sets. Time is their enemy. We should help them defeat it."

- Brota and Worf

"There's something else the other Odo wanted you to know, he was responsible for changing the Defiant's flight plan."
"Why?"
"So that you wouldn't have to die."
"I can't believe it! Eight thousand people!"
"He did it for you, Nerys, he loved you."
"That makes it right?!?"
"I don't know. He thought so."

- the present day Odo and Kira

"Alright we'll make a quick survey, but if all we detect is some fungus, we're not beaming down."
"What if it's smart fungus?"

Writer Gary Holland got the idea for this show after seeing the second season episode "The Collaborator", which he also wrote. In that episode, when Kira tells Odo that she is in love with VedekBareil, Odo reacts a little strangely. In the episode itself, he says it is because he is surprised that it has taken Kira so long to realize her true feelings, but many viewers felt it to be the first indication of Odo's love for Kira. That is exactly how Holland interpreted the scene, and he decided that he wanted to write a story about their relationship, but he knew it couldn't just be a straightforward narrative; "We have no idea how old Odo is, so if he's in his early development, it might be a long time before he can admit to those kind of feelings. So I wondered, 'How can I get an older Odo into the story?'" Holland's answer was time travel. (Star Trek: Deep Space Nine Companion) Interestingly, before his Odo/Kira love story went into production, there were numerous other developments: in the third season episode "Fascination", Lwaxana Troi guessed that Odo was in love with Kira, and in "Heart of Stone", Odo openly acknowledged it. However, he came to terms with the fact that she would never feel for him what he felt for her in "Crossfire", and "A Simple Investigation" apparently confirmed that he had moved on. It was at this point in the story arc where Holland's pitch was picked up.

Originally, it was supposed to be Yedrin who caused the destruction of the colony, but Ira Steven Behr felt this was a missed opportunity, that it didn't create any kind of conflict between any of the characters, and as such, he suggested that it be Odo instead. Some of the writers felt that this was too "dark" a thing for a regular to do, especially the morally rigid Odo, but Behr argued that that sense of unexpected darkness was exactly the point; Behr was always keen to take any opportunity to darken the show and the characters in un-Star Trek like ways (such as Kira refusing to apologize to Silaran Prin in "The Darkness and the Light" for example, or Worf actually fulfilling Kurn's request to impale him with a dagger in "Sons of Mogh"), and this was simply another example of that ideology. Behr states, "On The Original Series or The Next Generation, they probably would have made it the scientist and there'd be no harm, no foul. Everyone's hands would have remained clean. But that wasn't a consideration here." (Star Trek: Deep Space Nine Companion)

The writing staff chose to end Kira's relationship with Shakaar Edon via an off-screen break-up in this episode. While this was motivated in part due to budgetary and scheduling difficulties that had limited actor Duncan Regehr to only being able to appear three times in as many seasons, Ira Steven Behr subsequently admitted that by having Shakaar become head of the Bajoran Republic in his first appearance and then begin a relationship with Kira in his second, the writers had left themselves with nowhere else to take the character, short of having him come into conflict with Sisko, a role which they felt was better-served by KaiWinn Adami. (Star Trek: Deep Space Nine Companion, p. 83)

The planting scenes were filmed at Ahmanson Ranch, near Ventura, California, but on the day of the shoot, there were gale force winds, and equipment trucks had to be used as wind blocks. It was so cold, that the crew were all wearing snow jackets, but the actors had to wear shirt-sleeves because it was supposed to be a beautiful day. Between takes, the actors had to be sprayed down to make it look like they were sweating. (Star Trek: Deep Space Nine Companion)

Paul Baillargeon composed the music for the episode. Referring to the score of the scene where the Defiant crew help the Gaians to farm; Baillargeon commented: "I did something where I did a whole cue where I got into a fugue-type thing that's nearly a jig. That's a perfect example of something I'd never heard on a Star Trek show. So I tried it and they said hey, that's very nice. But that could have been a no-no. I didn't know what to expect. The worst thing that could happen is they'd tell me you're really going overboard and it sounds like an ancient fair. It's not medieval but it's like Prokofiev stuff, a lot of flutes, a lot of violins". (The Music of Star Trek, p 194)

Neither Nana Visitor or Rene Auberjonois were overly happy with how their characters were written in this episode. According to Visitor, "I'm not a huge fan of that whole romantic storyline. I think it's much more interesting to have a real deep friendship without it becoming physical. I would have liked Odo and Kira to stay like that. I did think this episode was brilliant. But it isn't one of my favorites, because I just wasn't crazy about my part in it." Auberjonois was also a little displeased with his part; "He allows an entire civilization to just disappear in a blink. He could rationalize it because of his love, but it's a big thing. It's tricky. I'm still not sure about it, or what kind of message it sent to the audience." Ronald D. Moore, however, has the answer; "It tells the audience how deeply this man can love. He can love to the point that he will sacrifice an entire world for a woman." (Star Trek: Deep Space Nine Companion)

This episode aired the same day as Armin Shimerman's first appearance on Buffy the Vampire Slayer, where he would continue as a reoccurring character for the next two seasons. Shimerman has said that on at least three occasions he worked on both shows on the same day, getting into the makeup chair before dawn to shoot his scenes for DS9 in the morning, then getting out of makeup in the early afternoon and driving an hour across town to shoot scenes for Buffy late into the night.

This episode presents a paradox: if Odo had been infected with the morphogenic virus previously, then he could not have grown 200 years older on the surface of the planet. He would have died of the virus a few years later. However it could be that the barrier somehow eliminated the virus, though ultimately it was never explained. It is possible that Odo was cured when he had his shapeshifting abilities taken away in "Broken Link" and was then infected again in "Behind the Lines", where he links with the female Founder.

An additional paradox is present. In the first iteration of the Defiant going into the past the crew were not aware of the planet's civilization - having never encountered it, because it didn't yet exist. If the second iteration occurred they would have been aware, so a simple repetition of the circumstances leading to the Children of Time was never possible. So, it was never possible to maintain the timeline in the first place unless they also received some sort of memory wipe (at least) in the second iteration of the return.

To convince Sisko that he is who he claims to be, Yedrin mentions a particular dancer that both Ben and Curzon Dax met on Pelios Station, which was previously alluded to in "Facets". The short story "The Music Between the Notes", from The Lives of Dax compilation, tells the full story of Sisko, Dax and the dancer.